General Structure Information
| PDB ID | 2e9w |
| HGNC Gene Label(s) | KIT |
| Structure Name | crystal structure of the extracellular domain of kit in complex with stem cell factor (scf) |
| Resolution | 3.5Å |
| Reference | AUTH S.YUZAWA,Y.OPATOWSKY,Z.ZHANG,V.MANDIYAN,I.LAX,J.SCHLESSINGERTITL STRUCTURAL BASIS FOR ACTIVATION OF THE RECEPTOR TYROSINETITL 2 KINASE KIT BY STEM CELL FACTORREF CELL(CAMBRIDGE,MASS.) V. 130 323 2007REFN ISSN 0092-8674PMID 17662946DOI 10.1016/J.CELL.2007.05.055 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 468 |
| Number Of SNVs | 88 |
| Number Of Permutations | 33195 |
| Optimal Distance Threshold | 12.0 |
| K Statistic | 0.045 |
| p-value | 0.188 |
COSMIC
| Number Of Residues | 468 |
| Number Of SNVs | 24 |
| Number Of Permutations | 27222 |
| Optimal Distance Threshold | 79.0 |
| K Statistic | 0.565 |
| p-value | 0.25 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 88 |
| Number Of COSMIC SNVs | 16 |
| Optimal Distance Threshold | 8.0 |
| K Statistic | 0.024 |
| p-value | 0.251 |
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:55561711 | rs55755457 | P>L | A:34 | (18.14, -23.24, 119.25) |
| 4:55561728 | H>Y | A:40 | (-2.59, -20.50, 115.85) | |
| 4:55561729 | rs373374682 | H>R | A:40 | (-2.59, -20.50, 115.85) |
| 4:55561731 | COSM1540224 | P>T | A:41 | (-3.06, -20.92, 112.38) |
| 4:55561737 | K>E | A:43 | (-3.03, -24.46, 108.99) | |
| 4:55561750 | I>T | A:47 | (-7.94, -20.83, 102.26) | |
| 4:55561755 | COSM1212554 | R>C | A:49 | (-14.42, -17.64, 101.68) |
| 4:55561764 | rs121913505 | D>N | A:52 | (-12.88, -12.90, 105.55) |
| 4:55561765 | COSM1212556 | D>G | A:52 | (-12.88, -12.90, 105.55) |
| 4:55561767 | E>K | A:53 | (-10.43, -11.64, 110.26) | |
| 4:55561769 | E>D | A:53 | (-10.43, -11.64, 110.26) | |
| 4:55561781 | L>F | A:57 | (-0.04, -15.59, 116.81) | |
| 4:55561785 | T>A | A:59 | (4.46, -17.91, 119.89) | |
| 4:55561809 | rs139441923 | T>S | A:67 | (7.73, -10.83, 106.67) |
| 4:55561810 | rs144933028 | T>S | A:67 | (7.73, -10.83, 106.67) |
| 4:55561831 | rs147943899 | T>M | A:74 | (7.59, -6.37, 101.03) |
| 4:55561840 | rs371353189 | N>S | A:77 | (4.55, -6.50, 111.86) |
| 4:55561861 | rs201872586 COSM3380948 |
T>M | A:84 | (-5.99, -8.54, 108.11) |
| 4:55561911 | H>Y | A:101 | (18.38, -16.83, 117.74) | |
| 4:55561914 | COSM139519 COSM1056093 |
G>S | A:102 | (17.14, -16.45, 112.61) |
| 4:55561927 | S>F | A:106 | (5.88, -19.88, 107.24) | |
| 4:55561929 | I>V | A:107 | (1.48, -19.45, 107.02) | |
| 4:55564461 | rs189660852 | L>I | A:117 | (-7.82, -16.06, 90.13) |
| 4:55564480 | rs371303702 COSM317523 |
S>F | A:123 | (6.76, -8.10, 83.92) |
| 4:55564500 | COSM1567314 | N>D | A:130 | (16.97, -19.28, 80.85) |
| 4:55564506 | T>A | A:132 | (11.21, -17.69, 82.73) | |
| 4:55564507 | COSM3409367 | T>M | A:132 | (11.21, -17.69, 82.73) |
| 4:55564515 | R>C | A:135 | (5.61, -12.70, 87.92) | |
| 4:55564532 | D>E | A:140 | (-8.37, -20.83, 94.71) | |
| 4:55564542 | T>A | A:144 | (-8.74, -28.08, 87.46) | |
| 4:55564569 | G>R | A:153 | (-6.44, -18.56, 70.11) | |
| 4:55564575 | P>S | A:155 | (-1.20, -22.12, 69.26) | |
| 4:55564576 | rs367719489 | P>L | A:155 | (-1.20, -22.12, 69.26) |
| 4:55564584 | K>E | A:158 | (5.63, -27.00, 70.43) | |
| 4:55564585 | K>M | A:158 | (5.63, -27.00, 70.43) | |
| 4:55564590 | COSM1694405 | L>M | A:160 | (6.86, -23.85, 75.28) |
| 4:55564594 | R>K | A:161 | (7.92, -26.35, 78.20) | |
| 4:55564624 | M>T | A:171 | (8.90, -21.83, 85.12) | |
| 4:55564633 | S>T | A:174 | (14.69, -23.01, 78.21) | |
| 4:55564644 | rs115585711 | A>T | A:178 | (11.55, -17.86, 69.24) |
| 4:55564674 | V>L | A:188 | (-7.66, -21.67, 85.55) | |
| 4:55564685 | E>D | A:191 | (-17.18, -23.93, 88.17) | |
| 4:55564698 | L>M | A:196 | (-7.90, -16.43, 80.84) | |
| 4:55565816 | V>M | A:214 | (34.31, -6.14, 63.10) | |
| 4:55565838 | Y>C | A:221 | (43.10, 5.94, 56.12) | |
| 4:55565871 | T>M | A:232 | (34.10, 4.54, 60.79) | |
| 4:55565883 | rs374957554 | K>T | A:236 | (27.14, -5.93, 62.93) |
| 4:55565909 | T>A | A:245 | (37.57, -0.18, 71.26) | |
| 4:55565910 | COSM1430117 | T>M | A:245 | (37.57, -0.18, 71.26) |
| 4:55565925 | N>S | A:250 | (50.96, -1.71, 70.81) | |
| 4:55569890 | T>A | A:253 | (45.26, 5.19, 75.56) | |
| 4:55569904 | COSM261692 | E>D | A:257 | (35.14, 6.64, 70.17) |
| 4:55569954 | rs138585275 | T>M | A:274 | (33.71, 7.52, 64.16) |
| 4:55569962 | I>L | A:277 | (42.68, 12.80, 63.96) | |
| 4:55569972 | rs386833402 COSM447951 |
A>V | A:280 | (47.47, 15.11, 61.32) |
| 4:55569975 | rs147367441 | R>K | A:281 | (49.79, 16.98, 63.90) |
| 4:55569977 | V>I | A:282 | (53.93, 12.88, 61.24) | |
| 4:55570011 | rs137909416 | N>S | A:293 | (34.41, -7.96, 74.03) |
| 4:55570035 | V>A | A:301 | (39.59, -4.46, 62.86) | |
| 4:55570043 | rs202052259 | T>A | A:304 | (47.49, 1.65, 58.54) |
| 4:55570049 | E>K | A:306 | (51.61, 6.75, 55.72) | |
| 4:55573282 | rs377590954 | I>N | A:315 | (60.38, 7.94, 39.01) |
| 4:55573287 | P>S | A:317 | (62.32, 3.18, 35.07) | |
| 4:55573292 | M>I | A:318 | (62.07, 0.12, 32.51) | |
| 4:55573295 | rs377102206 | I>M | A:319 | (65.58, -0.50, 30.56) |
| 4:55573302 | rs147540142 | T>A | A:322 | (69.74, 4.19, 26.54) |
| 4:55573317 | D>N | A:327 | (64.72, 4.38, 9.64) | |
| 4:55573337 | L>F | A:333 | (59.24, 5.31, 26.11) | |
| 4:55573383 | I>V | A:349 | (59.60, 17.02, 26.47) | |
| 4:55573394 | rs372759291 | N>K | A:352 | (63.65, 21.24, 26.05) |
| 4:55573418 | E>D | A:360 | (48.84, 5.68, 26.93) | |
| 4:55573429 | rs375734891 | K>R | A:364 | (49.54, -0.36, 37.90) |
| 4:55573444 | S>N | A:369 | (44.85, 2.82, 47.83) | |
| 4:55575609 | rs376275305 | L>I | A:379 | (57.94, 6.73, 19.70) |
| 4:55575613 | T>M | A:380 | (55.14, 5.75, 15.51) | |
| 4:55575627 | T>A | A:385 | (66.18, 13.10, 12.10) | |
| 4:55575645 | T>A | A:391 | (61.65, 14.11, 28.87) | |
| 4:55575669 | rs143707288 | V>I | A:399 | (57.02, 18.00, 43.98) |
| 4:55575673 | rs72549294 | N>S | A:400 | (58.23, 19.33, 40.60) |
| 4:55575675 | A>T | A:401 | (59.56, 15.31, 38.53) | |
| 4:55575691 | N>S | A:406 | (68.89, 9.23, 25.81) | |
| 4:55575702 | rs111646246 | N>Y | A:410 | (70.31, 3.12, 14.28) |
| 4:55589773 | COSM1166767 CD054354 |
D>N | A:419 | (85.84, 12.50, -4.49) |
| 4:55589794 | L>V | A:426 | (90.51, 6.70, -4.65) | |
| 4:55589830 | COSM1430125 | I>V | A:438 | (85.06, 1.63, 5.05) |
| 4:55589849 | P>L | A:444 | (86.97, -6.29, -12.33) | |
| 4:55592027 | rs145183977 | S>P | A:451 | (83.36, -9.10, -8.89) |
| 4:55592070 | S>F | A:465 | (83.71, 15.93, 17.32) | |
| 4:55592084 | G>R | A:470 | (75.07, 11.87, 15.76) | |
| 4:55592085 | G>E | A:470 | (75.07, 11.87, 15.76) | |
| 4:55592089 | K>N | A:471 | (74.25, 10.89, 11.27) | |
| 4:55592133 | N>S | A:486 | (90.75, -2.70, -16.84) | |
| 4:55592138 | T>P | A:488 | (85.79, -1.48, -11.36) | |
| 4:55592139 | rs56225530 | T>M | A:488 | (85.79, -1.48, -11.36) |
| 4:55592141 | COSM133784 | V>I | A:489 | (87.18, 0.25, -7.43) |
| 4:55592154 | rs371078350 | A>V | A:493 | (79.60, 1.01, 3.83) |
| 4:55592162 | rs143179681 | D>N | A:496 | (74.24, -3.30, 11.51) |
| 4:55592175 | rs200127012 | T>I | A:500 | (76.00, 1.70, 0.71) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:55561756 | COSM351040 | R>P | A:49 | (-14.42, -17.64, 101.68) |
| 4:55561758 | COSM42898 | V>M | A:50 | (-13.01, -12.22, 99.97) |
| 4:55561764 | COSM1146 | D>N | A:52 | (-12.88, -12.90, 105.55) |
| 4:55561765 | COSM1212556 | D>G | A:52 | (-12.88, -12.90, 105.55) |
| 4:55561801 | COSM4125147 | V>A | A:64 | (11.79, -9.96, 115.53) |
| 4:55561828 | COSM1430106 | E>G | A:73 | (3.70, -6.25, 97.46) |
| 4:55561845 | COSM3849654 | Q>K | A:79 | (3.00, -6.85, 116.55) |
| 4:55564480 | COSM317523 | S>F | A:123 | (6.76, -8.10, 83.92) |
| 4:55564485 | COSM3301424 | Y>H | A:125 | (11.54, -8.72, 80.92) |
| 4:55564501 | COSM1430112 | N>S | A:130 | (16.97, -19.28, 80.85) |
| 4:55564516 | COSM3301425 | R>H | A:135 | (5.61, -12.70, 87.92) |
| 4:55565895 | COSM1753772 | S>T | A:240 | (23.60, -3.21, 72.34) |
| 4:55565910 | COSM1430117 | T>M | A:245 | (37.57, -0.18, 71.26) |
| 4:55569904 | COSM261692 | E>D | A:257 | (35.14, 6.64, 70.17) |
| 4:55573315 | COSM1430119 | N>S | A:326 | (66.20, 0.84, 13.58) |
| 4:55573345 | COSM1618912 | E>V | A:336 | (56.23, 2.67, 36.46) |
| 4:55575669 | COSM51494 | V>I | A:399 | (57.02, 18.00, 43.98) |
| 4:55589774 | COSM1430124 | D>G | A:419 | (85.84, 12.50, -4.49) |
| 4:55589780 | COSM1272082 | L>H | A:421 | (93.14, 12.12, -3.97) |
| 4:55592042 | COSM19264 | P>S | A:456 | (93.12, -2.30, 1.25) |
| 4:55592043 | COSM1430126 | P>L | A:456 | (93.12, -2.30, 1.25) |
| 4:55592081 | COSM24637 | F>L | A:469 | (74.25, 14.09, 18.49) |
| 4:55592132 | COSM24639 | N>D | A:486 | (90.75, -2.70, -16.84) |
| 4:55592144 | COSM327599 | E>K | A:490 | (82.83, -1.02, -5.19) |
| 4:55592160 | COSM19028 | N>I | A:495 | (75.73, -0.40, 9.69) |
| 4:55592163 | COSM33971 | D>V | A:496 | (74.24, -3.30, 11.51) |
| 4:55592186 | COSM1430133 | F>I | A:504 | (85.34, 4.33, -7.58) |
| 4:55592192 | COSM96867 | F>L | A:506 | (92.60, 2.31, -12.08) |